Help! Definiition of superfamily, family, subfamily - eattch3.wav [1/1]

Chris Chetland rawmo at ihug.co.nz
Tue Apr 23 10:36:00 EST 1996


In article <4ielqv$p49$1 at mhade.production.compuserve.com>, 
102063.2640 at CompuServe.COM says...
>
>There are three further points that I think are relevant to this 
>discussion (which used to seem like a settled issue). 
>(1) Since so many interesting proteins are chimeras, we should 
>really refer ONLY to the domains (or predicted domains) as being 
>members of families, superfamilies, etc., rather than the proteins 
>that comprise them; "family" membership does connote common descent <- (This 
Whole Bit's Dodgy Bob, Tautologies are handy for proving/examining against, 
but pretty dull in many cases otherwise),
>and in many cases only a portion of a multi-domain protein can 
>properly be referred to in this sense. 
>(2) Since the primary distinction between a protein family and a 
>superfamily is the degree to which a functional activity (or set of 
>activities) is conserved, it is inappropriate to draw a firm 
>conclusion based on sequence comparisons IN THE ABSENCE OF PROTEIN 
>FUNCTIONAL INFORMATION.  This is not necessarily as important a 
>distinction for GENE families/superfamilies though, since their 
>functions can be more completely inferred from their sequences. 
>(3) It's never been clear to me just how we should relate the 
>concepts of protein family/superfamily, etc., to those of gene 
>family/superfamily, etc.(How about not bothering, less fun for an ordering 
mind, but maybe more realistic/less abstractly categorising?)  And what about 
pseudogenes, synthetic 
>genes, and knockouts?  And how should we NAME families?  The current
>practice is to use the name of the first family member discovered, 
>usually a poor choice.
>
>Bob Obar
>102063,2640 at compuserve.com
>102063,2640 at compuserve.com

Dearest Bob,
	 Have you ever considered that the concept of 'function' when refering 
to organisms may in fact be irrelevant?   1)What would you say about the ide 
that Organisms are UNCAUSED! The ascribing of the concept of function to 
either them, or particular 'separatable' aspects of them by which they 
comprise the whole brings with it a baggage that encompasses the ideas of an 
intelligent external creative force  as well as falling into a great many of 
the problems associated with a teleological perspective (the ultimate value of 
teleology in science has yet to be resolved, but on the whole it doesn't seem 
to be too good a good plan as far as a lot of scientists reckon).Here's a 
plan, read more on stuff like the concept of function in biology and critiques 
on it, it's in the library.

Any way...
		You seem to believe in (2) that due to the 'fact' that "the 
primary distinction between a protein family and a superfamily is the degree 
to which a functional (there's that word again!) activity (or set of 
activities)is conserved, it is InApPrOpRiAtE to draw a firm conclusion based 
on the sequence comparisons IN ABSENCE OF PROTEIN FUNCTIONAL INFORMATION".WHY 
WHY WHY WHY WHY WHY WHY WHY WHY???????  Ever thought that this definition/idea 
of distinction in itself might just be crap, and as a consequence the 
inference that you make from this 'primary definition' might  also be to say 
the least, a bit dodgy.

Sorry for the flaming Bob, but I think you deserve it, feel free to 
counter-flame.
	Cheers
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